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Grenier V, Gonzalez E, Brereton NJB, Pitre FE. Dynamics of bacterial and archaeal communities during horse bedding and green waste composting. PeerJ 2023; 11:e15239. [PMID: 37159830 PMCID: PMC10163874 DOI: 10.7717/peerj.15239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.
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Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
| | - Emmanuel Gonzalez
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Nicholas JB Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Frederic E. Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montréal, Québec, Canada
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2
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Sphingobacterium faecale sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1T. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1T was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria–Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C15 : 0, summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) and iso-C17 : 0 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1T was affiliated with the genus
Sphingobacterium
and had the highest sequence similarity to
Sphingobacterium tabacisoli
h337T (97.0 %) and Sphingobacterium paucimobilis HER1398T (95.6 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain C459-1T and
S. tabacisoli
h337T were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1T from other
Sphingobacterium
species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1T represents a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium faecale sp. nov. is proposed, with strain is C459-1T (CGMCC 1.18716T=KCTC 82381T) as the type strain.
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Siddiqi MZ, Park HY, Kim GR, Cui CH, Jo YJ, Kim SC, Im WT. Production of the Minor Ginsenoside F2 from the PPD-mix-type Major Ginsenosides Using a Novel Recombinant Glycoside Hydrolase from Novosphingobium aromaticivorans. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0215-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kakumanu ML, Marayati BF, Wada-Katsumata A, Wasserberg G, Schal C, Apperson CS, Ponnusamy L. Sphingobacterium phlebotomi sp. nov., a new member of family Sphingobacteriaceae isolated from sand fly rearing substrate. Int J Syst Evol Microbiol 2021; 71:004809. [PMID: 33956595 PMCID: PMC8289205 DOI: 10.1099/ijsem.0.004809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium, designated type strain SSI9T, was isolated from sand fly (Phlebotomus papatasi Scopoli; Diptera: Psychodidae) rearing substrate and subjected to polyphasic taxonomic analysis. Strain SSI9T contained phosphatidylethanolamine as a major polar lipid, MK-7 as the predominant quinone, and C16 : 1ω6c/C16 : 1ω7c, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0 as the major cellular fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that SSI9T represents a member of the genus Sphingobacterium, of the family Sphingobacteriaceae sharing 96.5-88.0 % sequence similarity with other species of the genus Sphingobacterium. The results of multilocus sequence analysis using the concatenated sequences of the housekeeping genes recA, rplC and groL indicated that SSI9T formed a separate branch in the genus Sphingobacterium. The genome of SSI9T is 5 197 142 bp with a DNA G+C content of 41.8 mol% and encodes 4395 predicted coding sequences, 49 tRNAs, and three complete rRNAs and two partial rRNAs. SSI9T could be distinguished from other species of the genus Sphingobacterium with validly published names by several phenotypic, chemotaxonomic and genomic characteristics. On the basis of the results of this polyphasic taxonomic analysis, the bacterial isolate represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium phlebotomi sp. nov. is proposed. The type strain is SSI9T (=ATCC TSD-210T=LMG 31664T=NRRL B-65603T).
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Affiliation(s)
- Madhavi L. Kakumanu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Bahjat Fadi Marayati
- Department of Biology, University of North Carolina Greensboro, 235 Eberhart Bldg., Greensboro, North Carolina, USA
| | - Ayako Wada-Katsumata
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Gideon Wasserberg
- Department of Biology, University of North Carolina Greensboro, 235 Eberhart Bldg., Greensboro, North Carolina, USA
| | - Coby Schal
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Charles S. Apperson
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Loganathan Ponnusamy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
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Li Y, Wang S, Chang JP, Bian DR, Guo LM, Yang XQ. Sphingomonas corticis sp. nov., and Sphingobacterium corticibacterium sp. nov., from bark canker. Int J Syst Evol Microbiol 2020; 70:5627-5633. [PMID: 32924914 DOI: 10.1099/ijsem.0.004451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7T and 30C10-4-7T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418T, and strain 30C10-4-7T shows highest sequence similarity to Sphingobacterium arenae H-12T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7T is a novel member different from recognized species in the genus Sphingomonas. The main fatty acids and respiratory quinone detected in strain 36D10-4-7T are C18 : 1 ω7c and/or C18 : 1 ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7T, the major fatty acids and menaquinone are iso-C15 : 0, C16 : 1 ω7c and/or C16 : 1 ω6c and iso-C17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium. The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7T=CFCC 13112T=KCTC 52799T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7T=CFCC 13069T=KCTC 52797T) are proposed.
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Affiliation(s)
- Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Shengkun Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Ju-Pu Chang
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Dan-Ran Bian
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Li-Min Guo
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Xu-Qi Yang
- Puyang Academy of Forestry, Puyang 457000, PR China
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Siddiqi MZ, Srinivasan S, Park HY, Im WT. Exploration and Characterization of Novel Glycoside Hydrolases from the Whole Genome of Lactobacillus ginsenosidimutans and Enriched Production of Minor Ginsenoside Rg3( S) by a Recombinant Enzymatic Process. Biomolecules 2020; 10:biom10020288. [PMID: 32059542 PMCID: PMC7072194 DOI: 10.3390/biom10020288] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/29/2020] [Accepted: 02/07/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Several studies have reported that ginsenoside Rg3(S) is effective in treating metastatic diseases, obesity, and various cancers, however, its presence in white ginseng cannot be estimated, and only a limited amount is present in red ginseng. Therefore, the use of recombinant glycosidases from a Generally Recognized As Safe (GRAS) host strain is a promising approach to enhance production of Rg3(S), which may improve nutritional activity, human health, and quality of life. Method: Lactobacillus ginsenosidimutans EMML 3041T, which was isolated from Korean fermented pickle (kimchi), presents ginsenoside-converting abilities. The strain was used to enrich the production of Rg3(S) by fermenting protopanaxadiol (PPD)-mix-type major ginsenosides (Rb1, Rb2, Rc, and Rd) in four different types of food-grade media (1, MRS; 2, Basel Food-Grade medium; 3, Basel Food-Grade medium-I, and 4, Basel Food-Grade medium-II). Due to its tendency to produce Rg3(S), the presence of glycoside hydrolase in Lactobacillus ginsenosidimutans was proposed, the whole genome was sequenced, and the probable glycoside hydrolase gene for ginsenoside conversion was cloned. Results: The L. ginsenosidimutans EMML 3041T strain was whole genome sequenced to identify the target genes. After genome sequencing, 12 sets of glycoside hydrolases were identified, of which seven sets (α,β-glucosidase and α,β-galactosidase) were cloned in Escherichia coli BL21 (DE3) using the pGEX4T-1 vector system. Among the sets of clones, only one clone (BglL.gin-952) showed ginsenoside-transforming abilities. The recombinant BglL.gin-952 comprised 952 amino acid residues and belonged to glycoside hydrolase family 3. The enzyme exhibited optimal activity at 55 °C and a pH of 7.5 and showed a promising conversion ability of major ginsenoside Rb1→Rd→Rg3(S). The recombinant enzyme (GST-BglL.gin-952) was used to mass produce Rg3(S) from major ginsenoside Rb1. Scale-up of production using 50 g of Rb1 resulted in 30 g of Rg3(S) with 74.3% chromatography purity. Conclusion: Our preliminary data demonstrated that this enzyme would be beneficial in the preparation of pharmacologically active minor ginsenoside Rg3(S) in the functional food and pharmaceutical industries.
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Korea;
- AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Jungang-ro Anseong-si, Gyeonggi-do Anseong-si, Gyeonggi-do 17579, Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Korea;
| | - Hye Yoon Park
- National Institute of Biological Resources, Incheon 22689, Korea;
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Korea;
- AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Jungang-ro Anseong-si, Gyeonggi-do Anseong-si, Gyeonggi-do 17579, Korea
- Correspondence: ; Tel.: +82-31-6705335; Fax: +82-31-6705339
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7
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Niu X, Cui W, Cui M, Zhang X, Zhang S, Xu B, Gao M. Sphingobacterium solani sp. nov., isolated from potato stems. Int J Syst Evol Microbiol 2018; 68:1012-1017. [DOI: 10.1099/ijsem.0.002605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xinbin Niu
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Weiguo Cui
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Man Cui
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shuqing Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Bingliang Xu
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Miao Gao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Lee Y, Jin HM, Jung HS, Jeon CO. Sphingobacterium humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:4632-4638. [PMID: 28945541 DOI: 10.1099/ijsem.0.002345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultatively aerobic bacterium, designated strain D1T, was isolated from soil in South Korea. Cells of strain D1T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1T formed a phyletic lineage with Sphingobacterium hotanense XH4T within the genus Sphingobacterium. Strain D1T was most closely related to S. hotanense XH4T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603T (97.2 %), and the DNA-DNA relatedness level between strain D1T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1T (=KACC 18595T=JCM 31225T).
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Affiliation(s)
- Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Mi Jin
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Abstract
A Gram-reaction-negative, aerobic, nonmotile, nonspore-forming, and rod-shaped bacterial strain designated Gsoil 3017T was isolated from soil of ginseng field and investigated by phenotypic and phylogenetic analyses. Strain Gsoil 3017T grew at 10-37 °C (optimal growth at 30 °C) and at pH 5.5-8.0 (optimal growth at pH 7) on R2A and nutrient agar without additional NaCl as a supplement. Strain Gsoil 3017T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1, Rc, and Rd (the three dominant active components of ginseng) to F2 and C-K, respectively. Based on 16S rRNA gene phylogeny, the novel strain represents a new branch within the genus Mucilaginibacter family Sphingobacteriaceae, and clusters with Mucilaginibacter frigoritolerans FT22T (95.6%) and Mucilaginibacter gotjawali SA3-7T (95.6%). The G+C content of the genomic DNA was 48.7%. The predominant respiratory quinone was MK-7, and the major fatty acids were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major polar lipid was phosphatidylethanolamine. Strain Gsoil 3017T could be differentiated genotypically and phenotypically from other type strains of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter ginsenosidivorans sp. nov. is proposed, with the type strain Gsoil 3017T (=KACC 14954T = JCM 17081T).
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Affiliation(s)
- Minseok M Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), 333 Techno Jungang-daero, Hyeonpung-myeon, Dalseong gun, Daegu, 42988, Republic of Korea
| | - Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do, 17579, Republic of Korea
- Center for Genetic Information Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do, 17579, Republic of Korea.
- Center for Genetic Information Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do, 17579, Republic of Korea.
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Mucilaginibacter ginsenosidivorans sp. nov., Isolated from Soil of Ginseng Field. Curr Microbiol 2017; 74:1382-1388. [PMID: 28821948 DOI: 10.1007/s00284-017-1329-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
A Gram-reaction-negative, aerobic, nonmotile, nonspore-forming, and rod-shaped bacterial strain designated Gsoil 3017T was isolated from soil of ginseng field and investigated by phenotypic and phylogenetic analyses. Strain Gsoil 3017T grew at 10-37 °C (optimal growth at 30 °C) and at pH 5.5-8.0 (optimal growth at pH 7) on R2A and nutrient agar without additional NaCl as a supplement. Strain Gsoil 3017T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1, Rc, and Rd (the three dominant active components of ginseng) to F2 and C-K, respectively. Based on 16S rRNA gene phylogeny, the novel strain represents a new branch within the genus Mucilaginibacter family Sphingobacteriaceae, and clusters with Mucilaginibacter frigoritolerans FT22T (95.6%) and Mucilaginibacter gotjawali SA3-7T (95.6%). The G+C content of the genomic DNA was 48.7%. The predominant respiratory quinone was MK-7, and the major fatty acids were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major polar lipid was phosphatidylethanolamine. Strain Gsoil 3017T could be differentiated genotypically and phenotypically from other type strains of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter ginsenosidivorans sp. nov. is proposed, with the type strain Gsoil 3017T (=KACC 14954T = JCM 17081T).
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Siddiqi MZ, Choi GM, Kim MS, Im WT. Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water. Int J Syst Evol Microbiol 2017; 67:2665-2671. [PMID: 28809138 DOI: 10.1099/ijsem.0.001994] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A Gram-stain-negative, oxidase- and catalase-positive, strictly aerobic, non-gliding bacterial strain, designated as NPT, was isolated from lake water and subjected to a taxonomic study using a polyphasic approach. Colonies of strain NP5T were light-yellow-coloured, circular with regular margins, and opaque. Cells were rods, 0.2-0.5 µm wide and 1.2-3.0 µm long. Strain NP5T possessed β-glycosidase activity, which was responsible for its ability to convert ginsenosides Rb1, Rc and Rd (three main active components of ginseng) to ginsenoside F2. Phylogenetic study based on the 16S rRNA gene sequence put strain NP5T in a distinct lineage in the family Flavobacteriaceae, sharing less than 96.0 % sequence similarity with members of the closely related genera Chryseobacterium, Bergeyella, Epilithonimonas and 'Candidatus Amoebinatus'. The novel isolate showed the highest sequence similarity with the genus Chryseobacterium. Strain NP5T contained MK-6 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH, C18 : 0 3-OH, anteiso-C15 : 0 and C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) as major fatty acids. The DNA G+C content was 44.8 mol%. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The physiological, biochemical and taxonomical characteristics allowed the phenotypic differentiation of strain NP5T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate NP5T represents a novel genus and species in the family Flavobacteriaceae for which the name Daejeonia ginsenosidivorans gen. nov., sp. nov. is proposed. The type strain is NP5T (=KACC 18626T=LMG 29198T).
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Gyu-Min Choi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Mi-Sun Kim
- Clean Fuel Research Center, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Wan-Taek Im
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
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Mucilaginibacter hankyongensis sp. nov., isolated from soil of ginseng field Baekdu Mountain. J Microbiol 2017; 55:525-530. [PMID: 28664515 DOI: 10.1007/s12275-017-7180-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 10/19/2022]
Abstract
A Gram-negative, non-motile, aerobic, and rod-shaped bacterial strain designated as BR5-28T was isolated from the soil of a ginseng field at Baekdu Mountain Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BR5-28T grew at 10-42°C (optimum temperature, 30°C) and pH 5.5-8.5 (optimum pH, 7.0) on R2A agar medium without additional NaCl supplementation. Strain BR5- 28T exhibited β-glucosidase activity, which was responsible for its ability to transform the ginsenosides Rb1 and Rd (the two dominant active components of ginseng) to compound-K. Based on 16S rRNA gene phylogeny, the novel strain showed a new branch within the genus Mucilaginibacter of the family Sphingobacteriaceae, and formed clusters with Mucilaginibacter frigoritolerans FT22T (95.8%) and Mucilaginibacter gotjawali SA3-7T (95.7%). The G+C content of the genomic DNA was 45.1%. The predominant respiratory quinone was MK-7 and the major fatty acids were summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c), iso-C15:0 and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain BR5-28T was differentiated genotypically and phenotypically from the recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter hankyongensis sp. nov. is proposed, with the type strain BR5-28T (=KCTC 22274T =DSM 21151T).
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Lai WA, Hameed A, Liu YC, Hsu YH, Lin SY, Young CC. Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacterium
thermophilum Yabe et al. 2013. Int J Syst Evol Microbiol 2016; 66:5336-5344. [DOI: 10.1099/ijsem.0.001517] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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